The Hydration Structure of Methylthiolate from QM/MM Molecular Dynamics

Thiols are widely present in biological systems, most notably as the side chain of cysteine amino acids in proteins. Thiols can be deprotonated to form a thiolate, which affords a diverse range of enzymatic activity and modes for chemical modification of proteins. Parameters for modeling thiolates using molecular mechanical force fields have not yet been validated, in part due to the lack of structural data on thiolate solvation. Here, the CHARMM36 and Amber models for thiolates in aqueous solutions are assessed using free energy perturbation and QM/MM MD simulations. The hydration structure of methylthiolate was calculated from 1 ns of QM/MM MD (PBE0/def2-TZVP//TIP3P), which show that the water–S- distances are approximately 2 Å. The CHARMM thiolate parameters predict a thiolate S radius close to the QM/MM value and predict a hydration Gibbs energy of -331 kJ/mol, close to the experimental value of -318 kJ/mol. The cysteine thiolate model in the Amber force field underestimates the thiolate radius by 0.2 Å and overestimates the thiolate hydration energy by 119 kJ/mol because it uses the same Lennard-Jones parameters for thiolates as for thiols. A recent Drude polarizable model for methylthiolate with optimized thiolate parameters also performs well. SAPT2+ analysis indicates exchange repulsion is larger for the methylthiolate, consistent with it having a more diffuse electron density distribution in comparison to the parent thiol. These data demonstrate that it is important to define distinct non-bonded parameters for the protonated/deprotonated states of amino acid side chains in molecular mechanical force fields.